RetrogeneDB ID: retro_mmul_1939

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:31043456..31044109(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LIMS2
• Ensembl ID: ENSMMUG00000004179
• Aliases: None
• Description: LIM and senescent cell antigen-like-containing domain protein 2 [Source:RefSeq peptide;Acc:NP_001252623]

Sequence

>retro_mmul_1939
GGGCATCTCTACCAGCCTTGCCATATCGCGAGAAGGCCAAGGGCCTGGCACAAGTGTCTGGCACCTCAGCAGTGCCACTT
GGTCATTCATGAGCAGCCCCTCATGTTCAGGAACAGTGCCTGACACCCAGGCCACTTCAGCTGCATCCACTGTAGGAAGG
AGCTGACTGGCGAGGCCCATGAGCTGAAGGGTGAACTCTACTGCCTGCCCTGCATTTACAAGATGCTGTCCCTATTTTTA
GGGACTGCAGCCAGCCCATCAAGGGTCACGTAGTGAATACACTGGGCAAAGAGTGGTGGCATGCAGAGCTTTTTGCCCTG
AGCGTGAGAAGCCATTCCTGGGGCTCTGGCACTATGAGAAGAAGGGCCTGGCCTACTTTGAGATCCACTACAGCCAGCTC
TTTGGAACATCTGCAGCCATGAAGTCGGGTGACATGGTGTTGGTCCTCAACAAGGCCTGATGTGTGTGAACTGCTTCTCC
TGTTCCACCTGCAAAAGCAGGCTCACTCTGAAGATCAACTTTGTGGAGTTTGACATGAAGCCCGTGTGTAAAAGGTGCTA
GATAACTTCCTCCTGGAGCTGAAGAAGAGGCTGAAGAAGTCATTGGAACTCACATCTCACTAGGCCCAGCCCAAGTCTGG
GGACCTCAACTCT

Alignment

ORF - retro_mmul_1939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.73 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GHLCRPCHNREKAKGLGKYIC-QRCHLVIDEQPLMFRSDAYHPDHFNCTHCGKELTAEARELKGELYCLP
          GHL..PCH.........K....Q.CHLVI.EQPLMFR..A.HP.HF.C.HC.KELT.EA.ELKGELYCLP
Retrocopy GHLYQPCHIARRPRAWHKCLAPQQCHLVIHEQPLMFRNSA*HPGHFSCIHCRKELTGEAHELKGELYCLP

Parental  CHDKM-GVPICGACRRPIEGRVVNAL-GKQWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYNQLFG-D
          C..KM..VPI...C..PI.G.VVN.L.G.........C...EKPFLG..HYEKKGLAY.E.HY.QLFG..
Retrocopy CIYKM<AVPIFRDCSQPIKGHVVNTL<GQRVVACRAFCPEREKPFLGLWHYEKKGLAYFEIHYSQLFG<N

Parental  VCYNCSHVIEGDVVSALNKAWCVSCFSCSTCNSKLTLKNKFVEFDMKPVCKRC-YEKFPLELKKRLKKLS
          .C...SH......V.......CV.CFSCSTC.S.LTLK..FVEFDMKPVCKRC....F.LELKKRLKK..
Retrocopy IC---SHEVG*HGVGPQQGLMCVNCFSCSTCKSRLTLKINFVEFDMKPVCKRC<LDNFLLELKKRLKKSL

Parental  ELTSRKAQPKAADLNS
          ELTS..AQPK..DLNS
Retrocopy ELTSH*AQPKSGDLNS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.22 RPM	6.61 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	13.49 RPM
SRP007412_cerebellum	0.13 RPM	2.78 RPM
SRP007412_heart	0.00 RPM	105.52 RPM
SRP007412_kidney	0.00 RPM	15.38 RPM
SRP007412_liver	0.04 RPM	37.41 RPM
SRP007412_testis	0.00 RPM	4.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1939 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000003146	1 retrocopy	retro_mmul_2283,
Macaca mulatta	ENSMMUG00000004179	1 retrocopy	retro_mmul_1939 ,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,